scPDB - 1bdm entry

Protein Data Bank Entry:

PDB ID : 1bdm

Resolution :1.800 Å

Experimental Method : X-ray

Deposition Date : 1993-02-16

Activity from ChEMBL: What is pChEMBL ?

	Min	Mean	Median	Standard Deviation	Max	Count
pChEMBL:

List of CHEMBLId :

Binding Site :

Uniprot Annotation

Name:	Malate dehydrogenase
ID:	MDH_THETH
AC:	P10584
Organism:	Thermus thermophilus
Reign:	Bacteria
TaxID:	274
EC Number:	/

Chains:

Chain Name:	Percentage of Residues within binding site
B	100 %

Ligand binding site composition:

B-Factor:	21.312
Number of residues:	46
Including
Standard Amino Acids:	42
Non Standard Amino Acids:	0
Water Molecules:	4
Cofactors:
Metals:

Cavity properties

Ligandability	Volume (Å3)
0.829	810.000

% Hydrophobic	% Polar
33.75	66.25
According to VolSite

Ligand :

HET Code:	NAX
Formula:	C21H30N7O15P2
Molecular weight:	682.448 g/mol
DrugBank ID:	-
Buried Surface Area:	58.35 %
Polar Surface area:	364.33 Å2

Number of
H-Bond Acceptors:	19
H-Bond Donors:	8
Rings:	5
Aromatic rings:	2
Anionic atoms:	2
Cationic atoms:	1
Rule of Five Violation:	3
Rotatable Bonds:	11

Mass center Coordinates

X	Y	Z
47.421	26.2532	37.026

Binding mode :

What is Poseview ?

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Image generated by PoseView

Protein

Binding Site

Ligand

Interaction pattern

hydrophobic (CA)

aromatic (CZ)

hydrogen bond acceptor (O)

hydrogen bond acceptor/donor (OG)

hydrogen bond donor (N)

positively ionized (NZ)

negatively ionized (OD1)

metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT

Ligand	Protein		Interaction
Atom	Atom	Residue	Distance (Å)	Angle (°)	Type
N3A	N	GLY- 10	3.15	129.36	H-Bond (Protein Donor)	false
O2A	NE2	GLN- 14	3.07	162.88	H-Bond (Protein Donor)	false
O2A	N	GLN- 14	2.81	164.34	H-Bond (Protein Donor)	false
O2N	N	ILE- 15	2.95	164.48	H-Bond (Protein Donor)	false
C1D	CD1	ILE- 15	4.49	0	Hydrophobic	false
C5D	CD1	ILE- 15	4.08	0	Hydrophobic	false
C6N	CD1	ILE- 15	3.54	0	Hydrophobic	false
O3B	OE2	GLU- 41	2.52	149.75	H-Bond (Ligand Donor)	false
O2B	OE2	GLU- 41	3.45	129.29	H-Bond (Ligand Donor)	false
O2B	OE1	GLU- 41	2.5	168.41	H-Bond (Ligand Donor)	false
C2B	CD1	ILE- 42	4.42	0	Hydrophobic	false
C5D	CG1	VAL- 86	3.65	0	Hydrophobic	false
C1D	CG1	VAL- 128	4.34	0	Hydrophobic	false
N7N	O	VAL- 128	3.38	148.75	H-Bond (Ligand Donor)	false
O3D	N	ASN- 130	2.95	170.09	H-Bond (Protein Donor)	false
O2D	ND2	ASN- 130	2.82	132.95	H-Bond (Protein Donor)	false
C1D	CB	ASN- 130	4.39	0	Hydrophobic	false
N7N	O	MET- 154	3.4	158.5	H-Bond (Ligand Donor)	false
C4N	CE	MET- 154	4.07	0	Hydrophobic	false
C4N	CD2	LEU- 157	3.94	0	Hydrophobic	false
C5N	CB	ALA- 245	3.5	0	Hydrophobic	false
O7N	O	HOH- 784	2.74	169.06	H-Bond (Protein Donor)	false